RetrogeneDB ID: retro_atri_30

Retrocopy location

• Organism: Amborella (Amborella trichopoda)
• Coordinates: AmTr_v1.0_scaffold00039:3218338..3218557(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: AMTR_s00049p00194290
• Aliases: None
• Description: None

Sequence

>retro_atri_30
ATGATGCTCTCAAATGATAAGTGACTTCCTTTGGCAGAATTGGATAAAAGGAAGCACAAACTCAAGAGCCTTGTTCAATC
TCCTCAATTTCTTTTTTACAACTGTTAAATGCCAAGATTCTTTCACCATAATAATTGTGTTCAGCCACTCCCATCAGTCA
TTGTATGTCAAAATTGTCTAGCCTTATTGTGTCAGCCAACTAGGGCGAAAGTGAAACTT

Alignment

ORF - retro_atri_30 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.04 %
• Parental protein coverage: 87.21 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MVLSNDIDLLHPPAELEKRKHKLKRLVQSP-NSFFMDVKCQGCFNITTVFSHSQ-TVVVCGNCQTVLCQP
          M.LSND..L..P.AEL.KRKHKLK.LVQSP.N.FF..VKCQ..F.I..VFSHS...V.VC.NC...LCQP
Retrocopy MMLSNDK*L--PLAELDKRKHKLKSLVQSP>NFFFTTVKCQDSFTIIIVFSHSH<SVIVCQNCLALLCQP

Parental  TGGRARL
          T.....L
Retrocopy TRAKVKL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Amborella trichopoda was not studied using RNA-Seq expression data.

ChIP-Seq

Amborella trichopoda was not studied using ChIP-Seq data.

EST

Amborella trichopoda was not studied using EST data.

TSS

Amborella trichopoda was not studied using FANTOM5 data.

Lab

retro_atri_30 was not experimentally validated.

Homology

Retrocopy orthology:

Amborella trichopoda does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00049p00194290	1 retrocopy	retro_atri_30 ,
Aegilops tauschii	F775_26813	1 retrocopy	retro_atau_70,
Solanum tuberosum	PGSC0003DMG401028933	3 retrocopies	retro_stub_137, retro_stub_138, retro_stub_140,